In a recent interview for the New York Times "Arts Beat" column, Joss Whedon let slip that work is being done on a sequel to Doctor Horrible's Sing-Along Blog, saying that "We’ve got several songs near completion and we’ve got a very specific structure." Whedon said that doing a continuation of his cult webseries is definitely something he "has his heart into," but it's all a matter of having enough time:
"We’ve just all got jobs. And it’s not like Neil, Nathan and Felicia ain’t busy either. We get together at Christmas and family occasions, and then play each other our partial songs and go, “Yup, that’s still exactly as it was the last time we played it. We’re great.” It’s bad."
What with his work in the upcoming Avengers movie, as well as staying very much involved with the Buffy and Angel comics at Dark Horse, it's not surprising that he's feeling the time crunch!
Whedon also joked that the title of the Dr. Horrible sequel would be called “Dr. Horrible and the Kingdom of the Crystal Skull," but he should know better than to scare us poor Geeks like that.